Peptide-based vaccines use small peptide sequences derived from target proteins as epitopes to provoke an immune reaction. These vaccines are a result of an improved understanding of the molecular basis of epitope recognition, thereby permitting the development of rationally designed, epitope-specific vaccines based on motifs demonstrated to bind to human class I or class II major histocompatibility complex (MHC) molecules. Of particular interest has been the discovery of epitopes (peptides of eight to eleven amino acids) that are specifically recognized by T cells for prophylaxis and treatment of infectious diseases.
Peptide-based vaccines offer several advantages over conventional vaccines for treating and preventing infectious diseases. For one, peptide-based vaccines are safer because they lack an infectious potential. In addition, peptide-based vaccines have a relatively long shelf-life because they are chemically stable and can be predictably, rapidly, and inexpensively manufactured. Furthermore, peptide-based vaccines allow one to target an immune response to specific epitopes that are neither suppressive nor hazardous for the host. Lastly, peptide-based vaccines allow for the possibility of preparing a multi-pathogen vaccine.
One particular infectious disease in which peptide-based vaccines have considerable potential in treating and preventing is viral infections, including Orthopoxvirus infections such as smallpox. Even though the World Health Organization declared that smallpox from naturally occurring Variola virus was eradicated in 1980, it is still a potential threat because of bioterrorism.
Peptide-based vaccines are particularly promising with T cells. T cells are responsible for cellular-mediated immunity, which exist in adaptive immune systems. There are two subsets of T cells, CD4+T cells and CD8+T cells. Of particular interest are CD8+T cells, known as cytotoxic T lymphocytes (CTLs), because they kill other infected cells and secreted antiviral cytokines. Unlike antibodies produced by B cells, receptors on CTLs only recognize short, yet contiguous, sequences on foreign antigens (epitope) complexed with class I MHC molecules on the surface of a cell. CTLs are important in immunity against cytosolic pathogens, especially viruses.
Limitations in identifying class I MHC molecules include the difficulty in detecting pathogen-derived peptides eluted from class I MHC complexes and the lack of knowledge regarding MHC class I presentation of viral peptides. Fortunately, the rapid characterization of defined peptides that are critical to viral immunity, including smallpox, has been significantly enhanced by mass spectrometry (MS), which provides peptide sequence information at the femtomole level of sensitivity.
Although direct sequencing of naturally processed peptides bound to class I MHC molecules by liquid chromatography mass spectrometry (LC-MS) is established, identification of pathogen-derived peptides presents a formidable challenge due to the diverse range of low abundance peptides presented by class I MHC molecules. Strategies to reduce the complexity of the mixture prior to introduction into the mass spectrometer have often relied on multiple steps of reversed phase (RP) liquid chromatography. However, this approach does not effectively increase the peak capacity because the separation mechanisms of each RP chromatography step are not orthogonal.
Accordingly, there is a renewed need for prophylaxis, therapeutics, and for diagnostics for Orthopoxvirus infections, particularly those that are based on the isolation of naturally processed viral peptides from class I MHC antigens.